Issues

• Speed-ups with identical outputs from profiling a 0.9M-nucleus multiome workflow: which would you like as PRs?

  bnprks/BPCells#344 · Filter by author koefoeden opened on Oct 21, 2026
  4

• open_matrix_anndata_hdf5() crashes (std::length_error: basic_string::_M_replace) reading .h5ad written by R's rhdf5/anndataR (STRPAD=NULLPAD/CSET=ASCII vlen strings)

  bnprks/BPCells#342 · Filter by author JuanTejedor opened on Jul 31, 2026

• Can't write to h5ad/h5

  bnprks/BPCells#341 · Filter by author smithcathy opened on Jun 25, 2026

• [ method on TransformLog1pSlow class throws an error on linux.

  bnprks/BPCells#340 · Filter by author Artur-man opened on Jun 21, 2026
  4

• Issue building from source for R

  bnprks/BPCells#333 · Filter by author verdurin opened on Feb 20, 2026

• Issues with threading

  bnprks/BPCells#327 · Filter by author jetrz opened on Dec 4, 2025
  2

• Matrix limit crash during merge on IterableMatrix

  bnprks/BPCells#325 · Filter by author sara-leka opened on Dec 2, 2025
  1

• mask_matrix invert = T not working

  bnprks/BPCells#324 · Filter by author Wenhe-Lin opened on Nov 25, 2025
  1

• Reading non-integer matrices in python

  bnprks/BPCells#312 · Filter by author eyalbenda opened on Oct 22, 2025
  2

• cannot install BPCells package on Linux(Centos7)

  bnprks/BPCells#310 · Filter by author BoTang1 opened on Oct 15, 2025
  3

• Allow the use of relative paths in open_matrix_dir/open_fragments_dir

  bnprks/BPCells#309 · Filter by author bjmt opened on Sep 28, 2025
  1

• Peak Calling with macs2

  bnprks/BPCells#307 · Filter by author plbngl opened on Sep 23, 2025
  5

• matrix_stats() breaks with multiple threads in some cases, when single threaded still works

  bnprks/BPCells#306 · Filter by author immanuelazn opened on Sep 20, 2025

• matrix with no cells

  bnprks/BPCells#305 · Filter by author brgew opened on Sep 18, 2025
  1

• select_cells on RNA matrix

  bnprks/BPCells#297 · Filter by author yxsee opened on Aug 28, 2025
  2

• Converting Seurat object to on-disk after normalization

  bnprks/BPCells#294 · Filter by author srangasw-bandolab opened on Aug 20, 2025
  1

• RunCCA - can BPCells help reduce running time?

  bnprks/BPCells#286 · Filter by author EchoCode4Fun opened on Jul 6, 2025
  1

• Inconsistent genes scores in scATAC analysis

  bnprks/BPCells#260 · Filter by author plbngl opened on Jun 9, 2025
  7

• Potentially contributing to the Python API

  bnprks/BPCells#255 · Filter by author fuxialexander opened on May 6, 2025
  6

• Error: basic_ios::clear: iostream error

  bnprks/BPCells#254 · Filter by author nashchem opened on May 6, 2025
  3

• BPCells::svds crashes for threads > 1

  bnprks/BPCells#250 · Filter by author Artur-man opened on Apr 22, 2025
  3

• Bioconda version of R package available

  bnprks/BPCells#241 · Filter by author mfansler opened on Apr 15, 2025

• accurate and pass-effecient SVD method

  bnprks/BPCells#213 · Filter by author Zilong-Li opened on Mar 21, 2025
  3

• convert seurat object to BPCell

  bnprks/BPCells#205 · Filter by author aarebeca opened on Feb 24, 2025
  5

• scRNAseq + scTCRseq

  bnprks/BPCells#204 · Filter by author aarebeca opened on Feb 24, 2025
  1